VMD-L Mailing List

From: Rob (spamrefuse_at_yahoo.com)
Date: Tue Oct 17 2006 - 21:02:42 CDT

> Rob,
> At present, if you load only a volumetric
> dataset into a molecule, there isn't a way to
> set it's periodicity. The current implementation
> demands that you have some atomic coordinates
> loaded in the molecule before you can use the
> periodic display feature. If you load both an
> atomic structure (even a 1 atom placeholder) and
> a volumetric dataset, you will be able to set
> the a/b/c/alpha/beta/gamma periodic boundary
> information.

Thank you for your explanations.

The volumetric data (charge density in my case) is
related to a specific molecular structure. So what
I did before, was loading the structure into a
'new molecule' and subsequently loading the
volumetric data into another 'new molecule'.
Hence, I could not multiply the volumetric data,
as you described above.

Now, I have followed your advice: load the molecular
structure as a new molecule first. The ID-line in
the VMD-Main window says:
  Atoms 2
  Frames 1
  Vol 0
Then I choose "Load data into molecule..." to load
the volumetric data. The same ID-line in the
VMD-Main window now says:
  Atoms 2
  Frames 1
  Vol 1
However, nothing appears to be added to first loaded
picture in the display window....
>From the vmd-console, I can see that the volumetric
data is loaded:
  Info) Analyzing Volume...
  Info) Grid size: 161x161x161 (63 MB)
  Info) Total voxels: 4173281
  Info) Min: -0.000001 Max: 8.233295 Range:
8.233297
  Info) Computing volume gradient map for smooth
shading
  Info) Added volume data, name=CHGCAR : Charge
density

But the the display window does not seem to show it.

Moreover, the 'Graphical Representation' window does
not have the volumetric gadgets in the 'Draw style'
tab (e.g. Isovalue slider, Draw selector, Show
selector etc.).

Am I doing something wrong?

By the way, I'm using 1.8.5 precompiled for Linux
i386, downloaded from the VMD homepage.

Regards,
Rob.

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